Hi 
Sorry I could get back to this before 
Here is my sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] GO.db_2.5.0          RSQLite_0.9-4        DBI_0.2-5           
 [4] AnnotationDbi_1.14.1 Biobase_2.12.2       biomaRt_2.8.1       
 [7] gregmisc_2.1.1       gplots_2.8.0         caTools_1.12        
[10] bitops_1.0-4.1       gtools_2.6.2         gmodels_2.15.1      
[13] gdata_2.8.2         

loaded via a namespace (and not attached):
[1] MASS_7.3-14  RCurl_1.6-10 XML_3.95-0  
> 

Thanks for any suggestions...
Konika


From: Marc Carlson <mcarlson@...>
Subject: Re: Is GO.db out of date?
Newsgroups: gmane.science.biology.informatics.conductor
Date: 2013-03-14 20:02:36 GMT (5 days, 13 hours and 12 minutes ago)
Hi Konika,

In order to answer your question, I need to know which version of GO.db 
you are using.  Can you please provide the results from your sessionInfo() ?

GO.db is updated with every release.  So the current release was updated 
last fall.  The version in the development branch (which will become the 
release in a couple weeks), was updated last week.

   Marc

On 03/14/2013 05:58 AM, konika chawla wrote:
> Hi
> I am using GO.db package for finding GO terms for a given Id.
> I failed to find few of these for example : GO:0001200, GO:0001227, GO:0001228
>   I used the code :
> goterms<-unlist(eapply(GOTERM,function(x) x <at> Term))
> goterms<-as.matrix(goterms)
> which(rownames(goterms)=="GO:0001200")
>> integer(0)
> In The gene Ontology database "GO:0001200" is for "metal ion regulated sequence-specific DNA binding
RNA polymerase II transcription factor activity".
> I also found that GOA has 39117 GO terms while GO.db has 32255 GO terms. I checked the reference manual for
GO.db which says it is updated biannually but the last update is of April2012.
> I am wondering if it will be updated soon else please suggest any other package which has similar functionality.
> Or is there any error in the code ??
> Thanks
> Konika Chawla
> PhD Student
> Department of Biology
> NTNU
>
>
>
>
>
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>
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Konika Chawla
PhD Student
Department of Biology
NTNU 





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